df=read_xlsx("Data/sgRNA/Figure5/N100M_sequence_result/N100M_plot.xlsx") %>%
janitor::clean_names()
df <- df %>%
mutate(point_size = ifelse(ladder_type == "Intact", 3.5, 2.5))
ggplot(df, aes(x = monoisotopic_mass/1000, y = apex_rt,
color = log10(sum_intensity),
shape = ladder_type,
group = ladder_type)) +
geom_point(aes(size = point_size)) + # Map size to point_size inside aes()
geom_line(color = "gray34", alpha = 0.5) + # Add lines connecting points within the same ladder_type
scale_x_continuous(name = "Monoisotopic Mass (kDa)", breaks = seq(0, max(df$monoisotopic_mass, na.rm = TRUE), by = 2)) +
scale_y_continuous(name = "Retention Time (min)", limits = c(0,19), breaks = seq(0, 19, by = 2)) +
labs(color = "Log10(Intensity)", shape = "Ladder Type", size = "Ladder Type") + # Add size to legend
theme_classic() +
theme(
axis.title.x = element_text(size = 12),
axis.title.y = element_text(size = 12),
axis.text.x = element_text(size = 10),
axis.text.y = element_text(size = 10),
legend.title = element_text(size = 10),
legend.text = element_text(size = 10)
) +
scale_color_gradientn(colors = turbo(256)) + # Use turbo color scale for the color aesthetic
scale_size_identity() # Use the actual values in point_size for sizing
## Warning: Removed 4 rows containing missing values or values outside the scale range
## (`geom_point()`).
## Warning: Removed 4 rows containing missing values or values outside the scale range
## (`geom_line()`).

df=read_xlsx("Data/sgRNA/Figure5/N100N_sequence_result/N100N_plot.xlsx") %>%
janitor::clean_names()
df <- df %>%
mutate(point_size = ifelse(ladder_type == "Intact", 3.5, 2.5))
ggplot(df, aes(x = monoisotopic_mass/1000, y = apex_rt,
color = log10(sum_intensity),
shape = ladder_type,
group = ladder_type)) +
geom_point(aes(size = point_size)) + # Map size to point_size inside aes()
geom_line(color = "gray34", alpha = 0.5) + # Add lines connecting points within the same ladder_type
scale_x_continuous(name = "Monoisotopic Mass (kDa)", breaks = seq(0, max(df$monoisotopic_mass, na.rm = TRUE), by = 2)) +
scale_y_continuous(name = "Retention Time (min)", limits = c(0, 19), breaks = seq(0, 19, by = 2)) +
labs(color = "Log10(Intensity)", shape = "Ladder Type", size = "Ladder Type") + # Add size to legend
theme_classic() +
theme(
axis.title.x = element_text(size = 12),
axis.title.y = element_text(size = 12),
axis.text.x = element_text(size = 10),
axis.text.y = element_text(size = 10),
legend.title = element_text(size = 10),
legend.text = element_text(size = 10)
) +
scale_color_gradientn(colors = turbo(256)) + # Use turbo color scale for the color aesthetic
scale_size_identity() # Use the actual values in point_size for sizing
## Warning: Removed 2 rows containing missing values or values outside the scale range
## (`geom_point()`).
## Warning: Removed 2 rows containing missing values or values outside the scale range
## (`geom_line()`).

plot_mixture("Data/sgRNA/Figure5/N100_mixture_result/100NM_19/100NM19_plot.xlsx")
## New names:
## • `` -> `...8`
## • `` -> `...9`
## • `` -> `...10`
## • `` -> `...11`
## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels
## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels
plot_mixture("Data/sgRNA/Figure5/N100_mixture_result/100NM_55/100NM55_plot.xlsx")
## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels
## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels
plot_mixture("Data/sgRNA/Figure5/N100_mixture_result/100NM_91/100NM91_plot.xlsx")
## New names:
## • `` -> `...8`
## • `` -> `...9`
## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels
## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels
df = read_xlsx("Data/sgRNA/Figure5/N100_mixture_result/mixture_coverage.xlsx")
## New names:
## • `` -> `...4`
## • `` -> `...5`
## • `` -> `...6`
## • `` -> `...7`
## • `` -> `...8`
## • `` -> `...9`
df = head(df, 10)
ggplot(df, aes(x = sgRNA1_percentage, y = coverage, fill = sgRNA_type)) +
geom_bar(stat = "identity", position = position_dodge(width = 2.5), width = 2) +
labs(
x = "Percentage sgRNA1 in mixture(%)",
y = "Percent Sequence Coverage(%)",
fill = "sgRNA Type"
) +
scale_x_continuous(breaks = c(10, 30, 50, 70, 90)) +
theme_minimal() +
scale_fill_brewer(palette = "Set1")
